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Language Skills

R
Bash
Python
AWK
SQL
Perl

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Made with the R package pagedown.

Based on the Nick Strayer’s CV package; modified source code for this CV is available here.

Last updated on 2020-11-09.

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Kasia Kedzierska

I am a 3rd year PhD student at the University of Oxford. I am a comuptational biologist, i.e. I use Data Science and Statistical Machine Learning while answering biological questions related to cancer of the uterus. Specifically, I study chromatin organisation in endometrial cancer. I spend most of my time either in command line writing Bash/Awk scripts or analysing and visualising data n R/Python.

I like teaching and deeply believe in Open Science. I am the President of #NGSchool Society with which I’ve been organising Summer Schoools in Bioinformatics. During last year edition - #NGSchool2019: Machine Learning for Biomedicine we recorded and published some of the lectures. This year, becasue of the pandemic we switched to organising virtual events, like NGSseminars series.

Research Experience

DPhil Candidate

Church group @ Wellcome Centre for Human Genetics, Wedge group @ Big Data Institute

University of Oxford, UK

2022 - 2018

  • PhD project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer

Visiting Graduate Student

Ratan group

University of Virginia, USA

2018 - 2017

  • Developed SONiCS - a tool for genotyping short tandem repeats (STRs) profiled using capture assays.
  • Worked on the Master thesis - Analysis of the mutational burden across gene sets in cancer.

Visiting Graduate Student

Pemberton group

University of Virginia, USA

2017 - 2016

  • Worked on Epigenetic regulation in prostate cancer.
  • Performed experiments and analyzed data from RNA-seq, ATAC-seq, and ChIP-seq assays.

Research Assistant

Zebrafish Developmental Genomics

IIMCB, Warsaw, Poland

2016 - 2015

  • I worked on the project: Elucidating gene regulatory network of zebrafish heart development using genomics.
  • I was responsible for both computational and experimental aspects of the project.

Education

DPhil. Candidate, Genomic Medicine and Statistics

Nuffield Department of Medicine, Brasenose College

University of Oxford, UK

2022 - 2018

  • Project: Functional and evolutionary characterisation of chromatin organisation in endometrial cancer.
  • Wellcome Trust Studentship

M. Sc. Eng., Biotechnology

Warsaw University of Technology

Warsaw, Poland

2018 - 2015

  • Thesis: Analysis of the mutational burden across gene sets in cancer.
  • Thesis awarded the best Master thesis in Bioinformatics defended in 2018 title.

B. Sc. Eng., Biotechnology

Warsaw University of Technology

Warsaw, Poland

2015 - 2011

Publications

The MLH1 polymorphism rs1800734 and risk of endometrial cancer with microsatellite instability

N/A

N/A

2020

  • MLH1 promoter polymorphism, rs1800734, association with MSI EC risk.

Prognostic integrated image-based immune and molecular profiling in early-stage Endometrial Cancer

N/A

N/A

2020

  • Quantification of intraepithelial CD8+ cells improved upon the prognostic utility of the molecular EC classification in early-stage EC

Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development

Genome Research

N/A

2019

  • Regulation networks in heart developmnent in zebrafish.

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer

BMC Cancer

N/A

2018

  • DNA repair genes and androgen signalling in prostate cancer cell lines.

SONiCS: PCR stutter noise correction in genome-scale microsatellites

Bioinformatics

N/A

2018

Posters, and Talks

Analysis of the mutational burden across gene sets in cancer

Polish Bioinformatics Society Symposium

Cracow, Poland

2019

  • Invited talk

Differential mutation analysis across gene sets in cancers

The Biology of Genomes 2018

Cold Spring Harbor, NY, USA

2018

  • Poster

Epigenetic regulation of prostate cancer

Visiting Graduate Traineeship Program Grantees Symposium

Charlottesville, VA, USA

2017

  • Talk

Awards and honours

Best Master Thesis in Bioinformatics       

N/A

N/A

2019 - 2018

  • The Best Master Thesis defended in the field of Bioinformatics in 2018 in Poland.
  • Analysis of the mutational burden across gene sets in cancer Masther thesis defended at the Warsaw University of Technology; code for the analyses can be accessed github.com/kzkedzierska/cancers

Visiting Graduate Traineeship Program

N/A

N/A

2017 - 2016

  • The Visiting Research Graduate Traineeship Program offered 12-month research traineeships for outstanding, qualified students from the life sciences at selected institutions in the United States.

Grasz o Staz

N/A

N/A

2015

  • “Grasz o Staz” competition was a national, prestigious and highly competitive (1:25 success rate) scholarship program in Poland organized by PwC.

Teaching Experience

Online tutorials: Python for Data Science and Introduction to Python

NGSeminars

N/A

2020

Introduction to Managing Code with Git

Wellcome Centre for Human Genetics

N/A

2020 - 2019

  • I led a 2-hour introduction to working with Git. The session aims at highlighting the advantages of working with Git as well as providing participants knowledge how to use Git.

Unsupervised learning, Introduction to Python

#NGSchool2019: Machine Learning for Biomedicine

N/A

2019

  • Tutor for the Introduction to Python (3 h workshop) and for the Unsupervised learning (1,5 h lecture).
  • Materials for the Introduction to Python are available on github

Introduction to R

Wellcome Centre for Human Genetics

N/A

2019

  • 8 week course in Introduction to R, Data Manipulation, Data Visualisation and RNA-seq data analysis.
  • Materials available on github/kzkedziersa/r_intro

ATAC-seq workshop

#NGSchool2017: Single-cell Sequencing

N/A

2017

Attended Workshops, Summer Schools

Machine Learning Summer School

Imperial College London, University College Londn

London, United Kingdom

2019

  • 12-day intensive course on a variety of topics in machine learning.

Grants

Visegrad Grant to organize #NGSchool2020 - postponed until 2021

N/A

N/A

2021 - 2020

  • A platform to share expertise in the field of Next Generation Sequencing data analysis and general bioinformatics.

Visegrad Grant to organize #NGSchool2019

Visegrad Fund

N/A

2019

  • 23,500 EUR awarded towards organising #NGSchool2019 allowed to keep the cost of attenting the school to the minimum and record the lectures for broader access.

Non profit work

President

NGSchool Society

N/A

2021 - 2018

  • The goal of the Society is to promote and support science, with emphasis on computational biology.
  • President since 2019; Vice President 2018 - 2019